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Meindlhumer, S. (author), Brauns, Fridtjof (author), Finžgar, Jernej Rudi (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)
The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD...
journal article 2023
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Japaridze, A. (author), van Wee, R.G. (author), Gogou, C. (author), Kerssemakers, J.W.J. (author), van den Berg, D.F. (author), Dekker, C. (author)
The bacterial chromosome is spatially organized through protein-mediated compaction, supercoiling, and cell-boundary confinement. Structural Maintenance of Chromosomes (SMC) complexes are a major class of chromosome-organizing proteins present throughout all domains of life. Here, we study the role of the Escherichia coli SMC complex MukBEF...
journal article 2023
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Davidson, Iain F. (author), Barth, R. (author), Zaczek, Maciej (author), van der Torre, J. (author), Tang, Wen (author), Nagasaka, Kota (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Wutz, Gordana (author), Dekker, C. (author), Peters, Jan Michael (author)
In eukaryotes, genomic DNA is extruded into loops by cohesin<sup>1</sup>. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)<sup>2,3</sup> that have important roles in gene regulation and recombination during development and disease<sup>1,4–7</sup>. How CTCF...
journal article 2023
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Ryu, J.K. (author), Rah, S.H. (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Bonato, Andrea (author), Michieletto, Davide (author), Dekker, C. (author)
The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion...
journal article 2022
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Würthner, Laeschkir (author), Brauns, Fridtjof (author), Pawlik, G. (author), Halatek, Jacob (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological processes inherently involve multiple spatial and temporal scales and transition from one pattern to another...
journal article 2022
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Meindlhumer, S. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
The Min protein system is arguably the best-studied model system for biological pattern formation. It exhibits pole-to-pole oscillations in E. coli bacteria as well as a variety of surface wave patterns in in vitro reconstitutions. Such Min surface wave patterns pose particular challenges to quantification as they are typically only semi...
journal article 2022
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Brauns, Fridtjof (author), Pawlik, G. (author), Halatek, Jacob (author), Kerssemakers, J.W.J. (author), Frey, Erwin (author), Dekker, C. (author)
Self-organisation of Min proteins is responsible for the spatial control of cell division in Escherichia coli, and has been studied both in vivo and in vitro. Intriguingly, the protein patterns observed in these settings differ qualitatively and quantitatively. This puzzling dichotomy has not been resolved to date. Using reconstituted...
journal article 2021
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Loeff, L. (author), Kerssemakers, J.W.J. (author), Joo, C. (author), Dekker, C. (author)
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step...
journal article 2021
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Japaridze, A. (author), Gogou, C. (author), Kerssemakers, J.W.J. (author), Nguyen, Huyen My (author), Dekker, C. (author)
The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move...
journal article 2020
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Kim, E. (author), Kerssemakers, J.W.J. (author), Shaltiel, Indra A. (author), Haering, Christian H. (author), Dekker, C. (author)
Condensin, a key component of the structure maintenance of chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA<sup>1</sup>. It remains unclear, however, how condensin complexes work together to collectively package DNA into chromosomes. Here we use time-lapse single-molecule visualization to...
journal article 2020
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Wu, Fabai (author), Japaridze, A. (author), Zheng, X.Z. (author), Wiktor, J.M. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower...
journal article 2019
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Deshpande, S.R. (author), Spoelstra, W.K. (author), van Doorn, M.C. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
Liposomes, self-assembled vesicles with a lipid-bilayer boundary similar to cell membranes, are extensively used in both fundamental and applied sciences. Manipulation of their physical properties, such as growth and division, may significantly expand their use as model systems in cellular and synthetic biology. Several approaches have been...
journal article 2018
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Eeftens, J.M. (author), Bisht, Shveta (author), Kerssemakers, J.W.J. (author), Kschonsak, Marc (author), Haering, Christian H. (author), Dekker, C. (author)
Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual...
journal article 2017
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Moolman, M.C. (author), Tiruvadi Krishnan, S. (author), Kerssemakers, J.W.J. (author), de Leeuw, R. (author), Lorent, V.J.F. (author), Sherratt, David J. (author), Dekker, N.H. (author)
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood....
journal article 2016
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Moolman, M.C. (author), Tiruvadi Krishnan, S. (author), Kerssemakers, J.W.J. (author), Van den Berg, A. (author), Tulinski, P. (author), Depken, M. (author), Reyes-Lamothe, R. (author), Sherratt, D.J. (author), Dekker, N.H. (author)
The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli ?2-sliding clamp have been characterized in vitro, its in vivo stoichiometry and dynamics remain unclear. To probe both ?2-clamp...
journal article 2014
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Van Loenhout, M.T. (author), De Vlaminck, I. (author), Flebus, B. (author), Den Blanken, J.F. (author), Zweifel, L.P. (author), Hooning, K.M. (author), Kerssemakers, J.W. (author), Dekker, C. (author)
The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that...
journal article 2013
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Moolman, M.C. (author), Huang, Z. (author), Krishnan, S.T. (author), Kerssemakers, J.W.J. (author), Dekker, N.H. (author)
Background: Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this...
journal article 2013
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De Vlaminck, I. (author), Van Loenhout, M.T.J. (author), Zweifel, L. (author), Den Blanken, J. (author), Hooning, K. (author), Hage, S. (author), Kerssemakers, J. (author), Dekker, C. (author)
In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining...
journal article 2012
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Van Loenhout, M.T.J. (author), Kerssemakers, J.W.J. (author), De Vlaminck, I. (author), Dekker, C. (author)
We present a three-dimensional tracking routine for nondiffraction-limited particles, which significantly reduces pixel bias. Our technique allows for increased resolution compared to that of previous methods, especially at low magnification or at high signal/noise ratio. This enables tracking with nanometer accuracy in a wide field of view and...
journal article 2012
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Dekker, N.H. (author), Kerssemakers, J. (author), Lipfert, J. (author)
The invention concerns a method and apparatus for determining one or more characterizing features of a macromolecule, in particular torque and/or twist of nucleic acids like DNA, using magnetic fields.
patent 2011
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